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CHECK report for hopach on malbec1

This page was generated on 2020-04-15 12:04:18 -0400 (Wed, 15 Apr 2020).

Package 798/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hopach 2.46.0
Katherine S. Pollard
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/hopach
Branch: RELEASE_3_10
Last Commit: 5ce7636
Last Changed Date: 2019-10-29 13:07:31 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hopach
Version: 2.46.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:hopach.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings hopach_2.46.0.tar.gz
StartedAt: 2020-04-15 00:13:29 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:14:37 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 68.6 seconds
RetCode: 0
Status:  OK 
CheckDir: hopach.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:hopach.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings hopach_2.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/hopach.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hopach/DESCRIPTION’ ... OK
* this is package ‘hopach’ version ‘2.46.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘hopach’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
boot2fuzzy 9.300  0.000   9.332
makeoutput 8.400  0.016   8.445
bootplot   8.072  0.000   8.086
bootstrap  7.576  0.000   7.592
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/hopach.Rcheck/00check.log’
for details.



Installation output

hopach.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL hopach
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘hopach’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c Rdistances.c -o Rdistances.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c hdist.c -o hdist.o
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o hopach.so Rdistances.o hdist.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-hopach/00new/hopach/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘as.hdist’ in package ‘hopach’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hopach)

Tests output


Example timings

hopach.Rcheck/hopach-Ex.timings

nameusersystemelapsed
boot2fuzzy9.3000.0009.332
bootplot8.0720.0008.086
bootstrap7.5760.0007.592
correlationordering0.0280.0000.026
disscosangle0.0000.0000.001
distancematrix0.0080.0000.005
dplot0.0480.0040.051
hdist-class0.0080.0000.010
hopach0.3160.0040.318
hopach.internal000
hopach2tree0.1880.0040.192
labelstomss0.1560.0000.155
makeoutput8.4000.0168.445
prune1.7600.0001.762